I cycled the Wisconsin portion of the river this past summer and about half the Ilinois section. It was superb and wisconsin section and north ill essentially unspoiled as of yet but fantastic bays and bird sanctuaries. Wisconsin's Great river route is on the web under that name, you can get a complete color print out for free, strip maps and directions for the entire 250 or so miles. The Iowa side is esswentially much more hilly and has not been set up yet on rod that would be good cycling. The wisconsin side onlyhas a few spots where traffic gets tight and in some place could use a couple directional markers(mostly in larger towns where route gets confusing) but essentially follows the same road and has several rail/trail segments. Campgrounds are plentiful but beware and check ahead, the wisconsin river route maps list so camping that no longer exists in some town, especailly at northern terminus. Also, it would be best to travel north to south, (1) you go with the flow and (2) the shoulders on road when travelling north are not as good or in many case non-existing.
Illinois has maps for the entire state in segments but nothing printed specific on river route although it does describe and show the route(he first rail/trail segment in Illinois is actually paved blacktop and was quite impressive, also the illinois campgrounds suprized me, they were plentiful, biker friendly, clean, quiet and cheap with the best tent sights (rolling grass and trees like a good golf course) I havde encountered in hyears of travel.
There are other segment prin out you can get on web if you reserach the miss river route site(southern ill included to ten and missouri side.
It was fun to be able to just jump in the river on a hot day.
There is also the option of getting off the river, if you are coming south, in Tennessee and pedaling the Natchez Trace Parkway from just below NAshville to Natchez MIss, Print out maps also available on web at Natchez Trace Parkway site.
Michael